couple off the top of my head:
1) (based on a suggestion from a previous thread): get rid of the half orc, and half elf races. Add orc as a player race. Add the feats Elven Blood, and Orcish Blood as human-only, take at character creation only feats, mutually exclusive feats. Elven blood gives elfy stuff (low light vision, sleep resistance, etc), Orcish blood gives orcy stuff (darkvision, scent, uh.. poor hygene..). And for god's sake make the Orc and Orcish Blooded human characters balanced with the other races. +2 str is not the end of the world.
2) change the Barbarian class name to Berzerker. Barbarian indicates a person from a primitive culture, and isn't appropriate if you're not.. well.. a person from a primitive culture.
3) Make Toughness, Endurance, and Skill Focus not suck. Example: instead of +3hp, make toughness be +2 effective con for the purpose of determining Hp only. Make Endurance apply to everything endurancy- fatigue rolls for not sleeping (or extend how long you can go without sleep, or less the ammount of sleep you need in a night), etc. Skill focus should be +3 on one skill, or +2 on two related skills: Knowledge: Arcana and Spellcraft, Diplomacy and Sense Motive, Appraise and Profession, etc.
4) Add more feats that don't directly relate to killing, magic, or other directly tied into Adventuring things. The Education fear from the FRCS is a good example. As is Cosmopolitan.
5) Balance spells between classes better. Why can an arcane caster funnel negative energy but not postive? Why can an evil cleric make intelligent undead, but the Arch-Necromancer cannot without researching the cleric's spell? Why can't an enchanter Modify Memory but a bard can?